[Biopython-dev] Pull Request for Codon Alignment GSoC project

[Peter Cock]

On Fri, Nov 15, 2013 at 2:57 AM, Zheng Ruan <zruan1991 at gmail.com> wrote:
> Hi all,
>
> Since a beta version of biopython has been released, it might be safe to
> merge my GSoC work.

We'll normally only do minor bug fixes and documentation improvements
between a beta and final release, but this is perfect timing for getting your
work merged immediately after Biopython 1.63 is out.

(So far there have been no problems reported with the beta, and
we've fixed some newline issues when testing under Windows)

> I just made a pull request and there seems to be some
> problems when running the code in different platforms. In
> python2.7 and python3.3, the error message complains they
> cannot find CodonAlign module. I'm not sure why this happens.

Some discussion is on the pull request itself:
https://github.com/biopython/biopython/pull/259

> The dependency of Scipy and Numpy might also
> introduce some problems for the testing. Thanks!

We've got a mechanism for skipping tests when a dependency
is missing - the MissingExternalDependencyError and
MissingPythonDependencyError exceptions. You need
to use this in test_CodonAlign.py, see test_PDB.py etc.

Related to this we would need to install new dependencies
on some of the buildbot slaves and perhaps TravisCI.

Regards,

Peter